I used SQL Doc 2 to document every table and column in two, small, databases.

PROBLEM 1:
When I went to SSMS, I was surprised to see no ying-yang icon denoting pending changes.

Right-clicked the database and "Refresh" - NOTHING CHANGED.

In the SSC UI, nothing showed up.

Clicked the Refresh icon next to "Commit" and - THEY ALL SHOW UP!

It appears that the "changes detection" code doesn't engage when an outside agent makes a change...

PROBLEM 2:
One of the Extended Properties AFTER the commit is being presented as still having a pending change. Hit "Commit" again. And there it is again, still a Pending Change, identical to what it was before.

Perhaps there's a character in the Extended Property that is throwing the Compare off?

What do you need to assist your debugging?

Here's what is actually in the Entity Description IN THE DATABASE (looking exactly like it should):

The PASTED ORIGINAL was mangled when I posted this, so I added a carriage return after each of the lines under the equals-line so you can see it. Appears that although the presentation in the before-pane is correct, the preparation of the update and/or SVN itself, flattens the lines out if they don't have a CR, just an LF... (Just theorizing)

This is fixed in the next update to SQL Source Control (any build > 3.1.0.4731).

It looks like there was an issue with the polling query we used, so certain changes didn't show up. Incidentally, if you added the extended property through SSMS, the indicator wouldn't show up until you refresh either, so it wasn't just external modifications causing the problem.